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PROCHECK Operating Manual
Appendix A - Stereochemical parameters
The two tables in this appendix list the stereochemical parameters used in the
PROCHECK programs.
Stereochemical parameters of Morris et
al. (1992), derived from high-resolution protein structures.
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Stereochemical parameter | Mean value | Standard deviation
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| |
phi-psi in most favoured | |
regions of Ramachandran plot | >90% |
| |
chi1 dihedral angle: | |
gauche minus | 64.1 degrees | 15.7 degrees
trans | 183.6 degrees | 16.8 degrees
gauce plus | -66.7 degrees | 15.0 degrees
| |
chi2 dihedral angle | 177.4 degrees | 18.5 degrees
| |
Proline phi torsion angle | -65.4 degrees | 11.2 degrees
| |
Helix phi torsion angle | -65.3 degrees | 11.9 degrees
Helix psi torsion angle | -39.4 degrees | 11.3 degrees
| |
chi3 (S-S bridge): | |
right-handed | 96.8 degrees | 14.8 degrees
left-handed | -85.8 degrees | 10.7 degrees
| |
Disulphide bond separation | 2.0A | 0.1A
| |
omega dihedral angle | 180.0 degrees | 5.8 degrees
| |
Main-chain hydrogen | |
bond energy (kcal/mol)* | -2.03 | 0.75
| |
Calpha chirality: zeta | |
``virtual'' torsion angle | 33.9 degrees | 3.5 degrees
(Calpha-N-C-Cbeta | |
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* Evaluated using the Kabsch & Sander
(1983) method.
Main-chain bond lengths and bond angles, and their standard deviations, as
observed in small molecules (Engh & Huber,
1991). The atom-labelling follows that used in the X-PLOR
dictionary, with some additional atom types (marked with an asterisk) as
defined by Engh & Huber (1991).
a. Bond lengths
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Bond | X-PLOR labelling} | Value | sigma
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C-N | C-NH1 | (except Pro) | 1.329 | 0.014
| C-N | (Pro) | 1.341 | 0.016
| | | |
C-O | C-O | | 1.231 | 0.020
| | | |
Calpha-C | CH1E-C | (except Gly) | 1.525 | 0.021
| CH2G*-C | (Gly) | 1.516 | 0.018
| | | |
Calpha-Cbeta | CH1E-CH3E | (Ala) | 1.521 | 0.033
| CH1E-CH1E | (Ile,Thr,Val) | 1.540 | 0.027
| CH1E-CH2E | (the rest) | 1.530 | 0.020
| | | |
N-Calpha | NH1-CH1E | (except Gly,Pro) | 1.458 | 0.019
| NH1-CH2G* | (Gly) | 1.451 | 0.016
| N-CH1E | (Pro) | 1.466 | 0.015
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b. Bond angles
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Angle | X-PLOR labelling | Value | sigma
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C-N-Calpha | C-NH1-CH1E | (except Gly,Pro) | 121.7 | 1.8
| C-NH1-CH2G* | (Gly) | 120.6 | 1.7
| C-N-CH1E | (Pro) | 122.6 | 5.0
| | | |
Calpha-C-N | CH1E-C-NH1 | (except Gly,Pro) | 116.2 | 2.0
| CH2G*-C-NH1 | (Gly) | 116.4 | 2.1
| CH1E-C-N | (Pro) | 116.9 | 1.5
| | | |
Calpha-C-O | CH1E-C-O | (except Gly) | 120.8 | 1.7
| CH2G*-C-O | (Gly) | 120.8 | 2.1
| | | |
Cbeta-Calpha-C | CH3E-CH1E-C | (Ala) | 110.5 | 1.5
| CH1E-CH1E-C | (Ile,Thr,Val) | 109.1 | 2.2
| CH2E-CH1E-C | (the rest) | 110.1 | 1.9
| | | |
N-Calpha-C | NH1-CH1E-C | (except Gly,Pro) | 111.2 | 2.8
| NH1-CH2G*-C | (Gly) | 112.5 | 2.9
| N-CH1E-C | (Pro) | 111.8 | 2.5
| | | |
N-Calpha-Cbeta | NH1-CH1E-CH3E | (Ala) | 110.4 | 1.5
| NH1-CH1E-CH1E | (Ile,Thr,Val) | 111.5 | 1.7
| N-CH1E-CH2E | (Pro) | 103.0 | 1.1
| NH1-CH1E-CH2E | (the rest) | 110.5 | 1.7
| | | |
O-C-N | O-C-NH1 | (except Pro) | 123.0 | 1.6
| O-C-N | (Pro) | 122.0 | 1.4
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PROCHECK Operating Manual
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